Is EEF2 p.Gly95Ser (c.283G>A) pathogenic?

EEF2 p.Gly95Ser (c.283G>A) is classified Likely benign in EEF2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-13). AlphaMissense: likely benign (0.2046); Ultra-rare (popmax 0.0827%, afr).

How common is EEF2 p.Gly95Ser (c.283G>A) in the general population?

EEF2 p.Gly95Ser (c.283G>A) is ultra-rare (popmax 0.0827%, afr) (gnomAD).

What do computational predictors say about EEF2 p.Gly95Ser (c.283G>A)?

AlphaMissense predicts likely benign (score 0.2046) — an in-silico prediction, not a clinical call.

EEF2 p.Gly95Ser

c.283G>A · rs145985140 · VCV447303

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2046 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0827%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2046	likely benign
REVEL	0.379	indeterminate
SaProt	LLR -10.34	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2, phastCons 1
Regional constraint	o/e 1.24	unconstrained · MANE · 56 bp · p 0.22 · regional, not allelic
Overall
CADD	26.5	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0827% African / African-American · 62/74,980 alleles

Filtering AF 0.0661% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0602%

Overall 0.00496% 80/1,613,966 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0827%	1,209
Remaining individualsnot grpmax-eligible	0.0064%	15,626
European (non-Finnish)	0.0011%	90,768
South Asian	0.0011%	91,078

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: EEF2
Protein: p.Gly95Ser
Coding: c.283G>A
MANE Select: NM_001961
dbSNP: rs145985140
Type: single nucleotide variant
Location: chr19:3983227 (GRCh38)
Gene constraint: LOEUF 0.39 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 89.97 · 26 PDB
Residue 95: the tr-type g domain; a β-strand

Full EEF2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

EEF2 p.Ala237Thr Uncertain significance ★★ ⚠ same type
EEF2 p.Ala238Thr Uncertain significance ★★ ⚠ same type
EEF2 p.Ala338Gly Uncertain significance ★★ ⚠ same type
EEF2 p.Ala624Thr Uncertain significance ★★ ⚠ same type
EEF2 p.Ala808Val Uncertain significance ★★ ⚠ same type
EEF2 p.Arg633His Uncertain significance ★★ ⚠ same type
EEF2 p.Arg647His Uncertain significance ★★ ⚠ same type
EEF2 p.Arg726Trp Uncertain significance ★★ ⚠ same type

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/eef2-p-gly95ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown